- phenixbb - phenix-online.org

syntax and alternate conformations
by Mark Collins 28 May '08

28 May '08

Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \ occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }

3 6

Re: [phenixbb] problem with high Rfree
by Christina Bourne 28 May '08

28 May '08

Thank you very much for your help. I just wanted to follow up in how I'm progressing with this. I tried the things you suggested, as well as a variety of others, with no luck. It turns out that my 4mol/AU P41 twinned data is ACTUALLY 8mol/AU P212121. The packing in the AU has an almost 41 screw relating 4 mols to the other 4. When this operation is carried out, 2 mols overlay 2 others almost perfect, while the other 2 overlay the other 2 by 180 degrees. So my AU packing is a pseudo-41 with apparent twinning. (The b dimension did not need halving, so my cell is 2x the size, if that makes sense). The data refines very well as P212121, and Rfree drops like a rock. Again, thank you so much for your suggestions, and Phenix is really wonderful! Christina ----- Original Message ---- From: Pavel Afonine <pafonine(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Tuesday, May 20, 2008 1:51:42 AM Subject: Re: [phenixbb] problem with high Rfree Hi Christina, I usually observe similar R/Rfree behavior when I use LS target instead of maximum-likelihood. In fact, twin refinement in phenix.refine is based on LS target function. This is just to share my observations; it's not necessarily happening in your case. - How many of test reflections you have and how they are distributed in resolution bins? - Just out of curiosity: did you try to ignore twinning and run refinement with default target? - What if you don't run SA? - Did you try to play with target weights (try different values for wxc_scale and wxu_scale) to see how this affect the R-factors? - Are you using the latest (or one of) phenix.refine? - Did you try to fill in water? Could you send a log file: may be we could spot something outstanding... Pavel. On 5/19/2008 1:32 PM, Christina Bourne wrote: Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina ________________________________ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

OXT
by Rife, Christopher L 23 May '08

23 May '08

Should phenix.refine be able to handle OXT? I find it is moving the OXT atom ~2A from where it should be. Do I need to rename it or add a separate definition to the refinement? Thanks, Chris

2 3

IUCr Crystallographic Computing School 2008
by Ralf W. Grosse-Kunstleve 23 May '08

23 May '08

IUCr Crystallographic Computing School 2008 * Sharing our knowledge * Kyoto, Japan, August 18-23 http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html The IUCr Crystallographic Computing School 2008 school aims to bring together both computational methods developers and users interested in looking beyond the interface. The format of the school fosters exchange of ideas via formal lectures, afternoon tutorials, coding challenges and code comparison sessions. The world-wide crystallographic community (including macro- and small-molecule crystallography, powder diffraction, and small-angle scattering) is invited to an intensive session of working together and learning from each other. The schedule of the program is available via the web link above. Abstracts are being added. Thanks to support from sponsors, we have been able to keep the registration cost (including accommodation and meals) below 70,000 YEN (ca. 430 EUR, 665 USD). The number of attendees is limited to 80 students. For more information visit the web site above. The registration deadline is July 25th, 2008. Organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)

1 0

Shell variable SSH_Path not set
by shivesh kumar 23 May '08

23 May '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

1 0

NCS restraints
by Rife, Christopher L 22 May '08

22 May '08

I'm refining a twinned structure at 2.2A that has 6 copies in the ASU. I am using NCS, however the ncs restraints are so tight that they are keeping the chains identical even though this takes them out of the density. Are there any parameters I can adjust that will lessen the strength of these restraints? Taking away NCS completely is also not ideal. I guess I would like an equivalent of 'medium' or 'loose' NCS restraints as implemented in Refmac. Thanks, Chris

2 1

Re: [phenixbb] Any real space map-mask / NCS utility?
by Tom Terwilliger 22 May '08

22 May '08

Hi Partha, I think we don't have a tool for just what you want...but here is an idea given what you are trying: In coot build a short piece of polypeptide in the region where one ha site is located. Match the map in some way. Now rotate/translate this exact piece of chain over to your other sites and match the density there. Now use phenix.superpose_pdbs to find your ncs and put that in resolve. Good luck! -Tom t At 05:48 AM 5/22/2008, you wrote: >Hi, > >Apologies for the strange question. > >Since phenix has one fantastic tool for each kind of purpose, I was >wondering if there is something that could combine features of USF >Rave package for example.. basically the question arises from the >difficulty of finding NCS operators in some cases, if we have less >than three heavy atoms per molecule or map is too bad to build >something. > >I am trying to create a mask around a heavy atom site in the map, give >it a translation to the next heavy atom which is probably in the next >molecule, give a 6d rotation and use that in Resolve for NCS >averaging. > >Any suggestion / script would be greatly appreciated. > >Cheers, Partha > > >-- >MRC National Institute for Medical Research >Division of Molecular Structure >The Ridgeway, NW7 1AA, UK >Email: pchakra(a)nimr.mrc.ac.uk >Phone: + 44 208 816 2515 >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

1 0

Any real space map-mask / NCS utility?
by Partha Chakrabarti 22 May '08

22 May '08

Hi, Apologies for the strange question. Since phenix has one fantastic tool for each kind of purpose, I was wondering if there is something that could combine features of USF Rave package for example.. basically the question arises from the difficulty of finding NCS operators in some cases, if we have less than three heavy atoms per molecule or map is too bad to build something. I am trying to create a mask around a heavy atom site in the map, give it a translation to the next heavy atom which is probably in the next molecule, give a 6d rotation and use that in Resolve for NCS averaging. Any suggestion / script would be greatly appreciated. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

1 0

decrease number of refs in test set
by Mark A Saper 22 May '08

22 May '08

I have a data set with about 10% of the reflections in the test set. I want to retain this test set for further refinement in phenix, but I want to decrease the number of reflections to say 5%. Can this be done in phenix? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor, Biophysics and Department of Biological Chemistry University of Michigan 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 Research summary

2 1

phenix.twin_map_utils gives AttributeError: 'module' object has no attribute 'r_free_flags_params'
by Francis E Reyes 21 May '08

21 May '08

chem171-152-dhcp:exptl_fobs_phases_freeR_flags.mtz francisreyes$ phenix.twin_map_utils xray_data.file=exptl_fobs_phases_freeR_flags.mtz model=MR.1_pdbset1_refine_007.pdb unit_cell=73.5,73.5,114,90,90,90 space_group="P 41 21 2" twin_utils { input { unit_cell = 73.5 73.5 114 90 90 90 space_group = "P 41 21 2" xray_data { file_name = "exptl_fobs_phases_freeR_flags.mtz" obs_labels = None free_flag = None } model { file_name = "MR.1_pdbset1_refine_007.pdb" } } parameters { twinning { twin_law = None max_delta = 3 } } output { logfile = "twin_tools.log" map_coeffs_root = "MAP_COEFFS" obs_and_calc = "obs_and_calc.mtz" } } Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/command_line/ twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/twinning/ twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' Any ideas? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 3